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HadrienG / InSilicoSeq

:rocket: A sequencing simulator
https://insilicoseq.readthedocs.io
MIT License
176 stars 32 forks source link

Bio.Alphabet has been removed from Biopython #233

Closed Tgrandis closed 10 months ago

Tgrandis commented 1 year ago

I just installed InSilicoSeq and tried it out. I got warnings that some packages were missing (SciPy etc) but after installing those I got an error of a different kind. I have Python 3.10.10 on a Linux Mint machine.

Traceback (most recent call last): File "/home/cab/miniconda3/bin/iss", line 6, in from iss.app import main File "/home/cab/miniconda3/lib/python3.10/site-packages/iss/app.py", line 8, in from iss import generator File "/home/cab/miniconda3/lib/python3.10/site-packages/iss/generator.py", line 12, in from Bio.Alphabet import IUPAC File "/home/cab/miniconda3/lib/python3.10/site-packages/Bio/Alphabet/init.py", line 20, in raise ImportError( ImportError: Bio.Alphabet has been removed from Biopython. In many cases, the alphabet can simply be ignored and removed from scripts. In a few cases, you may need to specify the molecule_type as an annotation on a SeqRecord for your script to work correctly. Please see https://biopython.org/wiki/Alphabet for more information.

jtclaypool commented 11 months ago

Not sure if this will work for you but I solved this through the pip upgrade. The conda install wasn't working for me. Also, make sure you have the appropriate versions installed pip install --upgrade InSilicoSeq


install_requires=['numpy', 'scipy', 'biopython<=1.78',
                      'pysam>=0.15.1', 'future',
                      'joblib', 'requests']```
HadrienG commented 10 months ago

This was fixed in v1.5.1